Variant report

Variant	rs12875666
Chromosome Location	chr13:80422683-80422684
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs12429730	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1335281	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2027146	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2027147	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2027148	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2152226	0.84[ASN][1000 genomes]
rs34928706	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4628842	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs4885669	0.86[ASN][1000 genomes]
rs4885670	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4885676	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4885677	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6563137	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs713614	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs713615	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7319612	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7333650	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7333880	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7338949	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs74099556	0.83[AMR][1000 genomes]
rs7982512	0.80[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs7983143	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs7984156	0.80[CHB][hapmap];1.00[JPT][hapmap]
rs7990168	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7990447	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9530975	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9530976	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9530978	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9530979	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9530983	0.81[LWK][hapmap];0.86[MKK][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes]
rs9545235	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9545236	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9545242	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs9545246	0.84[AMR][1000 genomes]
rs9646080	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs970738	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043768	chr13:80398379-80447095	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv1048990	chr13:80419496-80456454	Enhancers Weak transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
3	nsv1044254	chr13:80419496-80457686	Enhancers Flanking Active TSS Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:80414400-80424000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr13:80420400-80422800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr13:80420600-80423600	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr13:80422200-80422800	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr13:80422400-80423600	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr13:80422400-80427200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr13:80422400-80427400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr13:80422600-80423800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr13:80422600-80425000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr13:80422600-80425200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr13:80422600-80426000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links